Genomic Data Analysis NGS data processing on the CLI and GUI

Description

Embark on a Journey of Genomic Analysis: Building Skills for Reproducible Research

In this course, we guide you through an example genomic analysis of high-throughput (NGS) sequencing data, empowering you with the skills required for reproducible research. The course is divided into three phases, each designed to enhance your understanding and proficiency in genomic data analysis.

Phase 1: GUI Phase (Introduction to Galaxy)

In this phase, you'll be introduced to Galaxy, a user-friendly web-based platform for genomic analysis. Familiarize yourself with the Galaxy interface and its functionalities, setting the stage for deeper exploration.

Phase 2: Linux and WSL Environment

Gain essential knowledge of the Linux operating system and the Windows Subsystem for Linux (WSL) environment. Discover the power and versatility of the command line interface, laying the foundation for advanced genomic data processing.

Phase 3: Genomic Data Analysis - NGS Data Processing on the Command Line

This phase focuses on genomic data analysis using the command line interface. Begin with an introduction to the Unix tool/pipe metaphor and understand its significance in handling large-scale NGS data. Learn the benefits of the command line approach over graphical user interfaces (GUIs) in terms of repetition, reproducibility, project organization, and scalability.

Repetition:

Understand the advantages of the command line interface when dealing with multiple input files. Discover how it simplifies repetitive tasks and scales effortlessly as the number of input files increases.

Reproducibility:

Explore how command-line tools enable greater reproducibility compared to GUIs. Modify parameters, regenerate downstream results, and maintain consistency in your analysis.

Project Organization:

As your data and results multiply, the effective organization becomes crucial. Learn how to strategically structure and manage your files in a consistent and coherent manner, facilitating efficient data handling.

Scaling from Desktops to Servers:

While GUIs excel in individual computer interactions, command-line interfaces offer seamless scalability to server-based computing. Discover how the command line environment empowers you to leverage the power of servers for your genomic analyses.

By the end of this course, you'll possess the knowledge and skills to conduct genomic analyses using the command line interface efficiently. Embrace the power of reproducible research and elevate your proficiency in the field of genomics.

Don't miss this opportunity to dive into the world of genomic analysis. Enroll now and embark on a transformative journey toward reproducible and impactful research.

What You Will Learn!

• The basics of Next Generation Sequencing and how it can be used for Differential gene expression analysis via RNA sequencing.
• Quality Control of NGS data
• Trimming the Reads of NGS Data
• Different tools for aligning reads to genome
• Differential Expression.
• Ultimately understand how technologies like RNA sequencing could be used to identify specific genes that can cause certain conditions.
• Heatmap Generation of Results
• Interpret the results of DEG's
• Understanding Bioinformatics Pipeline concept
• Use of Galaxy for NGS data processing

Who Should Attend!

• People generally interested in new research methdologies and would like to try them themselves!
• Beginner Bioinformaticians looking to understand the process of RNA sequencing
• People interested in researching the effects of different pathologies on gene expression or even how gene expression changes over the course of a cell's growth curve.
• People looking to carry out differential gene expression and gene ontology analysis.
• People who want to carry out bioinformatic analysis without the need for complex code.

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